dbSNP rs561202364: SLC2A8:p.Asp66Asn (chr9-127397515-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014580.5(SLC2A8):c.196G>A(p.Asp66Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000047 in 1,277,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D66Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)

Exomes 𝑓: 0.0000047 ( 0 hom. )

Consequence

SLC2A8
NM_014580.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.559

Publications

0 publications found

Variant links:

Genes affected

SLC2A8 (HGNC:13812): (solute carrier family 2 member 8) This gene belongs to the solute carrier 2A family, which includes intracellular glucose transporters. Based on sequence comparison, the glucose transporters are grouped into three classes and this gene is a member of class II. The encoded protein, like other members of the family, contains several conserved residues and motifs and 12 transmembrane domains with both amino and carboxyl ends being on the cytosolic side of the membrane. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

SLC2A8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.20979309).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014580.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC2A8	NM_014580.5	MANE Select	c.196G>A	p.Asp66Asn	missense	Exon 2 of 10	NP_055395.2
SLC2A8	NM_001271711.2		c.196G>A	p.Asp66Asn	missense	Exon 2 of 9	NP_001258640.1	Q5VVV9
SLC2A8	NM_001271712.2		c.-64+229G>A		intron	N/A	NP_001258641.1	A0A087WT42

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC2A8	ENST00000373371.8	TSL:1 MANE Select	c.196G>A	p.Asp66Asn	missense	Exon 2 of 10	ENSP00000362469.3	Q9NY64
SLC2A8	ENST00000373360.7	TSL:1	c.196G>A	p.Asp66Asn	missense	Exon 2 of 9	ENSP00000362458.3	Q5VVV9
SLC2A8	ENST00000954537.1		c.196G>A	p.Asp66Asn	missense	Exon 2 of 10	ENSP00000624596.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000305

AC:

AN:

32800

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000795

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000470

AC:

AN:

1277490

Hom.:

Cov.:

AF XY:

0.00000319

AC XY:

AN XY:

627464

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24904

American (AMR)

AF:

0.00

AC:

AN:

16580

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20048

East Asian (EAS)

AF:

0.00

AC:

AN:

28434

South Asian (SAS)

AF:

0.00

AC:

AN:

64450

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31442

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3938

European-Non Finnish (NFE)

AF:

0.00000387

AC:

AN:

1034718

Other (OTH)

AF:

0.0000378

AC:

AN:

52976

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.417

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.075

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.78

DEOGEN2

Benign

0.14

Eigen

Benign

-0.52

Eigen_PC

Benign

-0.43

FATHMM_MKL

Benign

0.65

LIST_S2

Benign

0.80

M_CAP

Pathogenic

0.49

MetaRNN

Benign

0.21

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.58

PhyloP100

0.56

PrimateAI

Pathogenic

0.80

PROVEAN

Benign

-0.21

REVEL

Benign

0.17

Sift

Benign

0.40

Sift4G

Benign

0.48

Polyphen

0.0040

Vest4

0.10

MutPred

0.48

Gain of helix (P = 0.0143)

MVP

0.77

MPC

0.19

ClinPred

0.12

GERP RS

4.5

PromoterAI

-0.043

Neutral

(source)

Varity_R

0.090

gMVP

0.31

Mutation Taster

=94/6

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over